MolNFT v1 · #174527 · protein
Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh)
7BY8: “Malate dehydrogenase from geobacillus stearothermophilus (gs-mdh)”. X-ray diffraction, 18 pockets (best druggability 0.87). MolNFT v1 #174527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BY8
- Type
- protein
- Length
- 1,225 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- A0A143T1U9
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 311 | 52% helix, 21% strand | A0A143T1U9 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 302 | 52% helix, 21% strand | A0A143T1U9 |
| D | Malate dehydrogenase (EC 1.1.1.37) | protein | 301 | 51% helix, 21% strand | A0A143T1U9 |
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.87 | 0.89 | 140 | empty |
| 2 | 157 | 0.77 | 0.94 | 26 | empty |
| 3 | 172 | 0.77 | 0.93 | 25 | empty |
| 4 | 646 | 0.68 | 0.77 | 63 | empty |
| 5 | 674 | 0.68 | 0.76 | 77 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2066 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2047 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1087 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1078 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 811 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7BY8 · Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A143T1U9
- Elsewhere: RCSB PDB 7BY8 · PDBe 7BY8 · UniProt A0A143T1U9
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